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- PDB-1vte: MOLECULAR STRUCTURE OF NICKED DNA. MODEL A4 -

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Basic information

Entry
Database: PDB / ID: 1vte
TitleMOLECULAR STRUCTURE OF NICKED DNA. MODEL A4
Components
  • DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*AP*CP*GP*CP*G)-3')
  • DNA (5'-D(*CP*GP*CP*GP*TP*T)-3')
  • DNA (5'-D(*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / NICKED
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAymani, J. / Coll, M. / Van Der Marel, G.A. / Van Boom, J.H. / Wang, A.H.-J. / Rich, A.
Citation
Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 1990
Title: Molecular structure of nicked DNA: a substrate for DNA repair enzymes.
Authors: Aymami, J. / Coll, M. / van der Marel, G.A. / van Boom, J.H. / Wang, A.H. / Rich, A.
#1: Journal: Biochemistry / Year: 1989
Title: Molecular structure of the netropsin-d(CGCGATATCGCG) complex: DNA conformation in an alternating AT segment.
Authors: Coll, M. / Aymami, J. / van der Marel, G.A. / van Boom, J.H. / Rich, A. / Wang, A.H.
#2: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 1987
Title: A bifurcated hydrogen-bonded conformation in the d(A.T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin.
Authors: Coll, M. / Frederick, C.A. / Wang, A.H. / Rich, A.
#3: Journal: Nature / Year: 1980
Title: Crystal structure analysis of a complete turn of B-DNA.
Authors: Wing, R. / Drew, H. / Takano, T. / Broka, C. / Tanaka, S. / Itakura, K. / Dickerson, R.E.
History
DepositionMay 21, 1990Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author / pdbx_entity_src_syn
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*AP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*TP*T)-3')
C: DNA (5'-D(*TP*TP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,2823
Polymers7,2823
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-5 kcal/mol
Surface area4340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.990, 44.030, 66.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*AP*CP*GP*CP*G)-3')


Mass: 3681.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*CP*GP*CP*GP*TP*T)-3')


Mass: 1800.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*TP*CP*GP*CP*G)-3')


Mass: 1800.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5 / Details: pH 5.00, VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDConc.NameCrystal-IDDetailsSol-IDVolume (Å3)
12WATER1311
25MPD1614
38MGCL21917
411NA CACODYLATE112110
514SPERMINE_HCL115113
617WATER118216
720MPD121219

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 3 Å / Num. obs: 553 / Observed criterion σ(F): 2

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Processing

Software
NameClassification
ULTIMAmodel building
NUCLSQrefinement
ULTIMAphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Highest resolution: 3 Å / σ(F): 2 /
RfactorNum. reflection
obs0.182 553
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 483 0 72 555

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